iiinova — where your digital self keeps evolving

Ask Erin / Dear Beth @askerindearbeth.bsky.social · 28/09/2026

Ep 41! Distance transforms are super handy ways to filter or measure objects in images- but what are they, and how can we make and understand them? Let @erinweisbart.bsky.social and @bethcimini.bsky.social guide you along the way!

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Understanding Distance Transformations and using them in CellProfiler: AskErinDearBeth Episode 41

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 23/09/2026

AE/DB turns 40 (episodes)! Lots of biology shows up as speckles (or, as we prefer to think of them, ~*~sparkles~*~), but what kinds of measures can we use to quantify that? Let @bethcimini.bsky.social and @erinweisbart.bsky.social show you a few! Had fun trying out PygWalker and Molab for this one!

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How Punctate Are My Cells? aka How Sparkly Are My Cells? - AskErinDearBeth Episode 40

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 03/09/2026

Ep 39 - the final part in our collaboration 3-part series! While we LOVE collaborations, sometimes they don't go as planned (though we hope our tips in parts 1-2 help!), and people are difficult. What then? @erinweisbart.bsky.social and @bethcimini.bsky.social have some tips to make it least-worst!

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Working with Difficult Collaborators - Working in Collaborations Part 3 - AskErinDearBeth Episode 39

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 21/08/2026

Ep 38 - sorry for the delayed post! It's a shame to make you wait 4 days for this episode, because it's SUCH a fun one - @bethcimini.bsky.social and @erinweisbart.bsky.social show how to run a custom Cellpose model in CellProfiler, and our pro-tips for training across channels. It's like magic!

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Running a Custom Cellpose Model in CellProfiler - AskErinDearBeth Episode 38

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 05/08/2026

Ep 37 - part 2 in our series on collaboration! @erinweisbart.bsky.social talks @bethcimini.bsky.social through tools and tricks that can help make your collaborations smoother and more successful for everyone.

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Working With Collaborators II - Tools for Collaborations - AskErinDearBeth Episode 37

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 20/07/2026

Episode 36 - better by the 3-dozen! It's another VIEWER QUESTION, which is always a delight. CellProfiler features come in all sorts of distribution types - normal, left-shifted, right-shifted, you name it. How do you handle that? @bethcimini.bsky.social and @erinweisbart.bsky.social try to answer!

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Cell Painting Feature Transformations - AskErinDearBeth Episode 36

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 07/07/2026

Episode 35! Being a bioimage analyst is ALL about collaboration, and no one is better at it than @erinweisbart.bsky.social . Listen to her and @bethcimini.bsky.social talk about how to set up your collaborations for success. More parts coming soon!

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Working with Collaborators - Part I - AskErinDearBeth Episode 35

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 22/06/2026

Ep 34! Our 2nd-ever VIEWER QUESTION, and we are still EXCITED about those! (You should ask us some!) How do we measure if our images are, y'know, good? Feels like it should be easy, but it isn't! @bethcimini.bsky.social and @erinweisbart.bsky.social go through the options, and why none is perfect:

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Interpreting CellProfiler's Image Quality Measurements - AskErinDearBeth Episode 34

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 08/06/2026

Ep 33 - want to keep up on all the resources on Cell Painting? @erinweisbart.bsky.social has made a listing of the ones she has made (and those made by others, but she's made a lot of them!) and shares it in this week's episode with @bethcimini.bsky.social . Check out all the pretty colors here!

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Guide to Cell Painting for Biologists - AskErinDearBeth Episode 33

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 26/05/2026

Ep 32 - a chat between @bethcimini.bsky.social and @erinweisbart.bsky.social about a vision for the future of microscopy data and AI - no surprise from us, we think the secret sauce is ALL THE METADATA. Learn why below!

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What Kinds of BioImaging Data Does AI Need? - AskErinDearBeth Episode 32

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 11/05/2026

Ep 31- do you have cells (or other big objects) full of speckles (or other little objects)? Want to get rid of spots touching the cell edge? Let @erinweisbart.bsky.social and @bethcimini.bsky.social tell you how to make that happen in CellProfiler! (Not sure why we're making things LESS sparkly...)

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Filtering Objects that Touch the Cell Edge in CellProfiler - AskErinDearBeth Episode 31

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 28/04/2026

Ep 30!!! Like Cell Painting, but miss specific stains? No reason you can't have your cake and image it too! Let @bethcimini.bsky.social and @erinweisbart.bsky.social tell you why nothing matters (and why that's actually AWESOME) when you're setting up Cell Painting.

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Modifying the Cell Painting Assay - AskErinDearBeth Episode 30

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 13/04/2026

We're turning 29 episodes old! Learn from @erinweisbart.bsky.social and @bethcimini.bsky.social about Pooled Cell Painting, Cell Painting's version of Optical Pooled Screening. It's high-throughput heaven!

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Introduction to Pooled Cell Painting - AskErinDearBeth Episode 29

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 30/03/2026

Ep 28 - part 3/3 in our thresholding series! Find out from @bethcimini.bsky.social and @erinweisbart.bsky.social why threshold correction factors and bounds are SO critical for making your workflows scale, and great ways to bring the biology you know into your workflow. Don't sleep on them!

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Thresholding in CellProfiler Part 3: Correction Factor and Limits - AskErinDearBeth Episode 28

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 16/03/2026

Ep 27- have you heard deep learning called a "black box"? It often is, but this week, @erinweisbart.bsky.social tells @bethcimini.bsky.social about a cool paper from the @assafzaritsky.bsky.social team (and Erin!) using DL to make Cell Painting even more powerful, but still interpretable. So fun!

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Interpretable Deep Learning Features in Cell Painting: Anomaly Profiles - AskErinDearBeth Episode 27

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 02/03/2026

Ep 26! A whole year of AE/DB - thanks for making this first year fantastic! Cont. our deep dive on thresholding from Ep 24, @bethcimini.bsky.social and @erinweisbart.bsky.social walk through the algorithms in CellProfiler and when you might use them - our math-free logic for picking the right one!

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Thresholding in CellProfiler Part 2: Picking the Right Algorithm - AskErinDearBeth Episode 26

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 17/02/2026

Extra special bonus - video of Erin and I in the same place! It does happen!

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Ask Erin / Dear Beth @askerindearbeth.bsky.social · 17/02/2026

Ep 25 - from our new AE/DB Bsky account! It's a great one from @erinweisbart.bsky.social - once we've done Cell Painting and gotten our data, how do we interpret the measurements into biology? She and @bethcimini.bsky.social walk you through it. PLUS, in honor of our silver episode, bonuses (1/2)

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Interpreting Cell Painting Features: Classic Cell Profiler Features - AskErinDearBeth Episode 25

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FocalPlane @focalplane.bsky.social · 16/02/2026

Check out this fun post from @bethcimini.bsky.social & @erinweisbart.bsky.social, where they interview each other about their popular image analysis video podcast, ‘Ask Erin/Dear Beth’ @askerindearbeth.bsky.social. Episodes are posted every 2 weeks (ish). focalplane.biologists.com/2026/02/16/a...

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Ask Erin/Dear Beth - an image analysis tips and tricks video podcast - FocalPlane

Ask Erin/Dear Beth - an image analysis tips and tricks video podcast -

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 02/02/2026

Ep 24 - Understanding your thresholding options is the diff between a win and a loss in SO MANY workflows - gain that intuition, and SO MUCH is easier. The 1st of 3 episodes discussing why - inspired by OUR FIRST REAL READER QUESTION. @erinweisbart.bsky.social and I are actual advice columnists now!

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Thresholding in CellProfiler Part 1: Adaptive Thresholding - AskErinDearBeth Episode 24

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Erin Weisbart @erinweisbart.bsky.social · 02/02/2026

We answered our first viewer-submitted question in our "advice column" podcast! Thresholding when some areas are bright and some are dark is easy in CellProfiler with just one setting! Part 1/3 of a series on thresholding so keep an eye out for more w/ @bethcimini.bsky.social youtu.be/ynrPqsOZVYE

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Thresholding in CellProfiler Part 1: Adaptive Thresholding - AskErinDearBeth Episode 24

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Erin Weisbart @erinweisbart.bsky.social · 26/01/2026

@bethcimini.bsky.social and I talk about the Cell Painting Assay a LOT, especially on our podcast Ask Erin/Dear Beth, so we figured it was about time to talk about what it actually is! youtu.be/9-d6DoHtgUY h/t @drannecarpenter.bsky.social #science #biology #cellpainting #microscopy #imageanalysis

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Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 20/01/2026

Ep 23 - So what actually IS CellPainting anyway? You may have heard of it if you're say, a fan of the @drannecarpenter.bsky.social - @shantanu-singh.cc lab (and who isn't????), but what, you know, is it? Let @erinweisbart.bsky.social break it down for you! youtu.be/9-d6DoHtgUY

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Introduction to the Cell Painting Assay - AskErinDearBeth Episode 23

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 05/01/2026

Ep 22 - while we all love CellProfiler (right??), we know that often the challenging part is handling the "bookkeeping" to get your data into it in the first place. @erinweisbart.bsky.social and I do a quick overview, and then point to great longer-form materials. Welcome to AE/DB 2026!

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Overview of CellProfiler's Input Modules - AskErinDearBeth Episode 22

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 22/12/2025

The videos from this year's I2K are now online! Check out the Ask Erin / Dear Beth "Ask Us Anything" below, or the whole conference at www.i2kconference.org Making these 24 (with bonuses) episodes might be the most fun thing I did in 2025 - see you with more AE/DB content in 2026!

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Image Analysis Ask Us Anything - A special LIVE Ask Erin/Dear Beth event!

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 22/12/2025

Episode 21 - when we talk about doing image augmentations for deep learning, what do we MEAN? @erinweisbart.bsky.social uses CellProfiler to demonstrate exactly how we transform images to make neural networks more robust. PLUS (1/2)

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Visualizing Common Deep Learning Image Augmentations - AskErinDearBeth Episode 21

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/12/2025

20 eps - wow! Today, @erinweisbart.bsky.social and I introduce BioimagingGuide.org, a fantastic resource we made in partnership with @bioimagingna.bsky.social , your guide to "what you don't know you don't know" about imaging and analysis. Friendly and in 4 languages (and counting!); check it today!

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Intro to the Bioimaging Guide - AskErinDearBeth Episode 20

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 24/11/2025

Was lovely to see many of you @ I2K! Despite having major FOMO about missing so much stuff this fall (GloBIAS! CytoData! FoundingGIDE! CBIAS!), conferences ARE usually a great way to find @erinweisbart.bsky.social and I. In Episode 19, we talk through great societies/meetings we think you'll enjoy!

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Conferences We've Attended Recently - AskErinDearBeth Episode 19

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 11/11/2025

Episode 18 - @erinweisbart.bsky.social and I hung out IRL at @sbi2.bsky.social, forgot to film TOGETHER, but did ask our friends hard-hitting interview questions. Silliness ensued! Want to hang with us? We're doing a LIVE AMA next week at I2K - Wed Nov 19th, 1PM EST. Sign up at i2kconference.org !

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Women on the Street Interviews: Hard Hitting Questions at SBI2 2025 - AskErinDearBeth Episode 18

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Erin Weisbart @erinweisbart.bsky.social · 11/11/2025

This week on AskErinDearBeth, @bethcimini.bsky.social and I ask some hard hitting questions, (wo)man-on-the-street-style, at SBI2 2025 conference. Let us know, what's *your* favorite CellProfiler feature? And chime in on the debate: confocal or wide field microscopy? youtu.be/99L2ESvAt5I

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Women on the Street Interviews: Hard Hitting Questions at SBI2 2025 - AskErinDearBeth Episode 18

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 27/10/2025

Episode 17 - perhaps my favorite yet. How do you write a forum.image.sc post that will get you the answers you need without revealing information you don't want to tell? @erinweisbart.bsky.social and I go through what the experts need to know to help you. Post your sci q's today on forum.image.sc !

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How to Write a Great Post on the Image.sc Forum - AskErinDearBeth Episode 17

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 14/10/2025

Episode 16 - Learn more about the Cell Painting Gallery, a free repository of nearly a petabyte of images and imaging data, curated by the incredibly talented @erinweisbart.bsky.social . Truly a goldmine for big-data lovers everywhere!

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The Cell Painting Gallery, an Overview - AskErinDearBeth Episode 16

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 29/09/2025

Episode 15 - do your images look, well, weird when you open them on your computer? Bad? Weird-and-bad? While we can't tell you EXACTLY what's going on, in this edition of Ask Erin/Dear Beth, @erinweisbart.bsky.social and I go over the most common "ugh, why does it look like THAT?" cases.

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Why Do My Scientific Images Look Ugly!? - AskErinDearBeth Episode 15

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 15/09/2025

Episode 14 - In which @erinweisbart.bsky.social gives us a FANTASTIC tour through CellProfiler's illumination correction modules, how and when to use different kinds of illumination correction, and more. So so useful!

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Illumination Correction in CellProfiler (Two Ways!) - AskErinDearBeth Episode 14

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Erin Weisbart @erinweisbart.bsky.social · 09/09/2025

While image analysis may be our primary focus, @bethcimini.bsky.social and I have many shared nerderies. Love of #GBBO is one of them. Hear about my family's Great British Bake Off fantasy league and a couple of our favorite recipes on this ~bonus~ episode of AskErinDearBeth! youtu.be/hKEO9UeP1yw

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Baking Nerds Talk GBBO - AskErinDearBeth Episode 13 5

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 02/09/2025

Episode 13 - so why is it so important to use the small brush in ilastik (ep 11)? How do random forests WORK, anyway? Join @erinweisbart.bsky.social and I as we explore using #marimo! Looking for notebooks/pipelines/images, or want to submit a q? Check our site! ciminilab.github.io/AskErin_Dear...

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How to Train a Pixel Classifier - AskErinDearBeth Episode 13

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 18/08/2025

Episode 12- my lucky number! Might become yours too if you have lots of cell outline images you need to make into masks - @erinweisbart.bsky.social shows you our plugin for this, along with SUCH a clever trick (that I never would have thought of) for cleaning up small and/or edge masks. Enjoy!

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Importing Objects from Outline Images in CellProfiler - AskErinDearBeth Episode 12

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 05/08/2025

Episode 11 - In which @erinweisbart.bsky.social and I talk about just how much we love ilastik (@ilastik-team.bsky.social) and how it's great for so many problems! Also, that you should use a small brush.

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Intro to Pixel Classification in ilastik - AskErinDearBeth Episode 11

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 22/07/2025

Episode 10 - we've jumped an order of magnitude! Thanks for all the support, @erinweisbart.bsky.social and I totally appreciate it. If you have artifact-free data, you can skip this one; for us mere mortals, Erin talks about masks, alignment, and seeing how far from a mask an object is. So useful!

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Images with 0's: Masks and measuring distances from 0's in CellProfiler - AskErinDearBeth Episode 10

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/07/2025

Episode 9 - maybe the #1 question we get on forum.image.sc is "how can I find cells and figure out what fraction are positive for marker X?". Since this is CellProfiler, we show you not 1 but 3 ways to do it, including a throwback to Ep 7. Let @erinweisbart.bsky.social and I help you get it done!

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AskErinDearBeth Episode 9 - Calculating Percent Positive in CellProfiler

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 23/06/2025

Episode 8 - CellProfiler does a lot, but could it do EVEN MORE? Hop on in to let @erinweisbart.bsky.social tell you all about CellProfiler plugins - where to find them, how to use them, and how they can add the Power Of Deep Learning to your local copy of CellProfiler!

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AskErinDearBeth Episode 8 - CellProfiler Plugins

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 09/06/2025

Episode 7 - want to add some sparkles (aka speckles) to your life? Check out @erinweisbart.bsky.social and my favorite tricks for modules and settings that make speckle finding a snap in CellProfiler on this week's episode of Ask Erin/Dear Beth!

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AskErinDearBeth Episode 7 - Identifying Speckles in CellProfiler

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Erin Weisbart @erinweisbart.bsky.social · 03/06/2025

I cannot overstate how amazing it is to work in a supportive, kind, collaborative environment and - even better - with my best friend. Scary times aren't quite as scary and we do better science. Beth and I talk about this in a recent AskErinDearBeth! youtu.be/9gKE9euaUJo

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AskErinDearBeth Bonus Episode 6.5 - In the beginning

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Erin Weisbart @erinweisbart.bsky.social · 03/06/2025

LoadData is how I bypass the use of my nemesis (the NamesAndTypes module) and a super handy way to pass file information and metadata into CellProfiler. Wanna hear me and Beth explain what it is and how to use it? Check out the latest episode of AskErinDearBeth!

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 02/06/2025

We decided to start with THE DEEP LORE - aka, how did Erin and I first meet and how did we begin on this wacky journey! If you want to know where the journey began, here's the opening chapter. (2/2)

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AskErinDearBeth Bonus Episode 6.5

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 02/06/2025

Gah! I was traveling last week and forgot to tell you re: Episode 6 - in which @erinweisbart.bsky.social and I dig into yet another way to get data into Cell Profiler, via CSV. Super useful for big data! But as a silver lining, I get to shout out our first BONUS EPISODE (1/2)

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AskErinDearBeth Episode 6 - Using Load Data in CellProfiler

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 15/05/2025

Episode 5 - sure, most cells have one nucleus, but what happens when they DON'T? @erinweisbart.bsky.social and I try to get to the bottom of what on earth you can do when your cells and nuclei just don't match up on the latest episode of "Ask Erin/Dear Beth"

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AskErinDearBeth Episode 5 - Handling multinucleate cells in CellProfiler

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 28/04/2025

Episode 4 - in which @erinweisbart.bsky.social and I fight the commonest @cellprofiler.bsky.social battle yet - with a million ways to read in your data, what is the right way for YOUR data? Shall a new hope arise? Will we find only one way to do things? Watch and find out!

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AskErinDearBeth Episode 4 - Proprietary File Formats in Fiji and CellProfiler

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 15/04/2025

New episode of Ask Erin/Dear Beth just dropped! See how Erin handles figuring out experiment quality and segmentation performance for multi-well plate data! See Beth force Erin to define things (very well!) she didn't want to define! Learn to ensure your large experiments have only the best vibes.

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Erin Weisbart @erinweisbart.bsky.social · 14/04/2025

Now out: Episode 3 of Ask Erin/Dear Beth in which @bethcimini.bsky.social and I overview the method we use for QC on high content imaging datasets. It's great for ~*~vibes~*~ and to QC segmentation along with catching debris, confluency, or focus issues. youtu.be/5pAcdd_Nn00

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AskErinDearBeth Episode 3 - QC on High Content Imaging Datasets using CellProfiler and FIJI

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